Crossref
journal-article
Elsevier BV
Journal of Molecular Biology (78)
References
78
Referenced
70
10.1093/nar/25.17.3389
/ Nucl. Acids Res. / Gapped BLAST and PSI-BLAST: a new generation of protein database search programs by Altschul (1997)10.1006/jmbi.1994.1104
/ J. Mol. Biol. / Hidden Markov models in computational biology. Applications to protein modeling by Krogh (1994)10.1089/cmb.1995.2.9
/ J. Comput. Biol. / Maximum discrimination hidden Markov models of sequence consensus by Eddy (1995)10.1016/S0959-440X(96)80056-X
/ Curr. Opin. Struct. Biol. / Hidden Markov models by Eddy (1996)10.1002/(SICI)1097-0134(1997)1+<134::AID-PROT18>3.0.CO;2-P
/ Proteins: Struct. Funct. Genet. / Predicting protein structure using hidden Markov models by Karplus (1997)10.1110/ps.9.2.232
/ Protein Sci. / Comparison of sequence profiles. Strategies for structural predictions using sequence information by Rychlewski (2000)10.1093/nar/gkg504
/ Nucl. Acids Res. / ORFeus: detection of distant homology using sequence profiles and predicted secondary structure by Ginalski (2003)10.1006/jmbi.2001.5293
/ J. Mol. Biol. / Within the twilight zone: a sensitive profile–profile comparison tool based on information theory by Yona (2002)10.1016/S0022-2836(02)01371-2
/ J. Mol. Biol. / COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance by Sadreyev (2003)10.1126/science.1853201
/ Science / A method to identify protein sequences that fold into a known three-dimensional structure by Bowie (1991)10.1038/358086a0
/ Nature / A new approach to protein fold recognition by Jones (1992)10.1006/jmbi.1993.1323
/ J. Mol. Biol. / Alignment and searching for common protein folds using a data bank of structural templates by Johnson (1993)10.1096/fasebj.10.1.8566533
/ FASEB J. / Assigning amino acid sequences to 3-dimensional protein folds by Fischer (1996)10.1006/jmbi.1997.1101
/ J. Mol. Biol. / Protein fold recognition by prediction-based threading by Rost (1997)10.1006/jmbi.1997.0924
/ J. Mol. Biol. / A 3D–1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence by Rice (1997)10.1002/(SICI)1097-0134(19990701)36:1<68::AID-PROT6>3.0.CO;2-1
/ Proteins: Struct. Funct. Genet. / Hidden Markov models that use predicted secondary structures for fold recognition by Hargbo (1999)10.1006/jmbi.2000.3741
/ J. Mol. Biol. / Enhanced genome annotation using structural profiles in the program 3D-PSSM by Kelley (2000)10.1006/jmbi.2001.4762
/ J. Mol. Biol. / FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties by Shi (2001)10.1002/pro.5560070620
/ Protein Sci. / Fold prediction by a hierarchy of sequence, threading, and modeling methods by Jaroszewski (1998)10.1006/jmbi.1999.2583
/ J. Mol. Biol. / GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences by Jones (1999)10.1006/jmbi.2000.3541
/ J. Mol. Biol. / Combination of threading potentials and sequence profiles improves fold recognition by Panchenko (2000)10.1002/prot.1080
/ Proteins: Struct. Funct. Genet. / Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement by Kolinski (2001)10.1002/(SICI)1097-0134(19990401)35:1<70::AID-PROT7>3.0.CO;2-9
/ Proteins: Struct. Funct. Genet. / Identification of homologous core structures by Matsuo (1999)10.1006/jmbi.1999.2911
/ J. Mol. Biol. / Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function by Mirny (1999)10.1006/jmbi.2000.3973
/ J. Mol. Biol. / An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance by Yang (2000)10.1002/1097-0134(20010201)42:2<148::AID-PROT20>3.0.CO;2-R
/ Proteins: Struct. Funct. Genet. / Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins by Reddy (2001)10.1016/S1093-3263(98)80002-8
/ J. Mol. Graph. Model. / Amino acid similarity matrix for homology modeling derived from structural alignment and optimized by the Monte Carlo method by Ogata (1998)10.1093/protein/13.8.545
/ Protein Eng. / Structure-derived substitution matrices for alignment of distantly related sequences by Prlic (2000)10.1006/jmbi.2001.4495
/ J. Mol. Biol. / Pairwise sequence alignment below the twilight zone by Blake (2001)10.1110/ps.19902
/ Protein Sci. / A comparison of position-specific score matrices based on sequence and structure alignments by Panchenko (2002)10.1073/pnas.011577898
/ Proc. Natl Acad. Sci. USA / Combining multiple structure and sequence alignments to improve sequence detection and alignment: application to the SH2 domains of Janus kinases by Al-Lazikani (2001)10.1006/jmbi.2001.5080
/ J. Mol. Biol. / Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure by Gough (2001)10.1006/jmbi.1995.0424
/ J. Mol. Biol. / Recurring local sequence motifs in proteins by Han (1995)10.1093/protein/11.11.981
/ Protein Eng. / Novel method to detect a motif of local structures in different protein conformations by Wako (1998)10.1006/jmbi.1998.1943
/ J. Mol. Biol. / Prediction of local structure in proteins using a library of sequence-structure motifs by Bystroff (1998)10.1006/jmbi.1999.2581
/ J. Mol. Biol. / Three-dimensional structure analysis of PROSITE patterns by Kasuya (1999)10.1006/jmbi.2001.4466
/ J. Mol. Biol. / Consistency analysis of similarity between multiple alignments: prediction of protein function and fold structure from analysis of local sequence motifs by Kunin (2001)10.1002/pro.5560050711
/ Protein Sci. / The structural alignment between two proteins: is there a unique answer? by Godzik (1996)10.1093/nar/27.1.220
/ Nucl. Acids Res. / PRINTS prepares for the new millennium by Attwood (1999)10.1093/nar/28.1.228
/ Nucl. Acids Res. / Increased coverage of protein families with the blocks database servers by Henikoff (2000)10.1093/nar/29.1.37
/ Nucl. Acids Res. / The InterPro database, an integrated documentation resource for protein families, domains and functional sites by Apweiler (2001)10.1016/0022-2836(80)90373-3
/ J. Mol. Biol. / How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins by Lesk (1980)10.1093/protein/1.3.159
/ Protein Eng. / Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modeling by Hubbard (1987)10.1002/pro.5560021104
/ Protein Sci. / Comparison of conformational characteristics in structurally similar protein pairs by Flores (1993)10.1006/jmbi.1994.1733
/ J. Mol. Biol. / Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility by Russell (1994)10.1006/jmbi.1999.2972
/ J. Mol. Biol. / Evolution of protein sequences and structures by Wood (1999)10.1006/jmbi.2000.3975
/ J. Mol. Biol. / An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments by Yang (2000)10.1006/jmbi.1999.3377
/ J. Mol. Biol. / Identification of related proteins on family, superfamily and fold level by Lindahl (2000)10.1093/nar/30.1.268
/ Nucl. Acids Res. / SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments by Gough (2002)10.1093/bioinformatics/18.9.1243
/ Bioinformatics / The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs by Griffiths-Jones (2002)10.1016/S0969-2126(00)00189-1
/ Struct. Fold. Des. / Crystal structure of Omp32, the anion-selective porin from Comamonas acidovorans, in complex with a periplasmic peptide at 2.1Å resolution by Zeth (2000)10.1038/nsb0198-37
/ Nature Struct. Biol. / Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose by Forst (1998)10.1126/science.7824948
/ Science / Structural basis for sugar translocation through maltoporin channels at 3.1Å resolution by Schirmer (1995)10.1110/ps.29402
/ Protein Sci. / Toward genomic identification of {beta}-barrel membrane proteins: composition and architecture of known structures by Wimley (2002)10.1002/pro.5560040820
/ Protein Sci. / Gibbs motif sampling: detection of bacterial outer membrane protein repeats by Neuwald (1995)10.1002/prot.10043
/ Proteins: Struct. Funct. Genet. / A study on protein sequence alignment quality by Elofsson (2002)10.1073/pnas.95.11.5865
/ Proc. Natl Acad. Sci. USA / Highly specific protein sequence motifs for genome analysis by Nevill-Manning (1998)10.1002/prot.10550
/ Proteins: Struct. Funct. Genet. / Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling by Petrey (2003){'key': '10.1016/j.jmb.2003.10.025_BIB59', 'series-title': 'Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids', 'author': 'Durbin', 'year': '1998'}
/ Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids by Durbin (1998)10.1093/bioinformatics/18.12.1658
/ Bioinformatics / Structure-dependent sequence alignment for remotely related proteins by Yang (2002)10.1093/nar/gkg619
/ Nucl. Acids Res. / EVA: evaluation of protein structure prediction servers by Koh (2003)10.1016/S0022-2836(05)80134-2
/ J. Mol. Biol. / SCOP: a structural classification of proteins database for the investigation of sequences and structures by Murzin (1995)10.1093/nar/28.1.257
/ Nucl. Acids Res. / SCOP: a structural classification of proteins database by Lo Conte (2000)10.1093/bioinformatics/btg224
/ Bioinformatics / PISCES: a protein sequence culling server by Wang (2003)10.1093/bioinformatics/18.1.77
/ Bioinformatics / Tolerating some redundancy significantly speeds up clustering of large protein databases by Li (2002)10.1093/bioinformatics/16.5.458
/ Bioinformatics / RSDB: representative protein sequence databases have high information content by Park (2000)10.1006/jmbi.1997.1287
/ J. Mol. Biol. / Do aligned sequences share the same fold? by Abagyan (1997)10.1073/pnas.81.4.1075
/ Proc. Natl Acad. Sci. USA / On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations by Kabsch (1984)10.1002/bip.360221211
/ Biopolymers / Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features by Kabsch (1983){'key': '10.1016/j.jmb.2003.10.025_BIB70', 'first-page': '21', 'article-title': 'The value of prior knowledge in discovering motifs with MEME', 'volume': '3', 'author': 'Bailey', 'year': '1995', 'journal-title': 'Proc. Int. Conf. Intell. Syst. Mol. Biol.'}
/ Proc. Int. Conf. Intell. Syst. Mol. Biol. / The value of prior knowledge in discovering motifs with MEME by Bailey (1995)10.1002/1097-0134(20000815)40:3<502::AID-PROT170>3.0.CO;2-Q
/ Proteins: Struct. Funct. Genet. / Application of multiple sequence alignment profiles to improve protein secondary structure prediction by Cuff (2000)10.1006/jmbi.1999.3091
/ J. Mol. Biol. / Protein secondary structure prediction based on position-specific scoring matrices by Jones (1999)10.1006/jmbi.1993.1413
/ J. Mol. Biol. / Prediction of protein secondary structure at better than 70% accuracy by Rost (1993)10.1073/pnas.95.11.6073
/ Proc. Natl Acad. Sci. USA / Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships by Brenner (1998)10.1093/nar/22.22.4673
/ Nucl. Acids Res. / CLUSTAL W.: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice by Thompson (1994)10.1016/S0076-6879(96)66024-8
/ Methods Enzymol. / Using CLUSTAL for multiple sequence alignments by Higgins (1996)10.1016/S0076-6879(96)66033-9
/ Methods Enzymol. / PHD: predicting one-dimensional protein structure by profile-based neural networks by Rost (1996){'key': '10.1016/j.jmb.2003.10.025_BIB78', 'first-page': '28', 'article-title': 'Fitting a mixture model by expectation maximization to discover motifs in biopolymers', 'volume': '2', 'author': 'Bailey', 'year': '1994', 'journal-title': 'Proc. Int. Conf. Intell. Syst. Mol. Biol.'}
/ Proc. Int. Conf. Intell. Syst. Mol. Biol. / Fitting a mixture model by expectation maximization to discover motifs in biopolymers by Bailey (1994)
Dates
Type | When |
---|---|
Created | 21 years, 8 months ago (Dec. 2, 2003, 8:23 a.m.) |
Deposited | 6 years, 6 months ago (Feb. 16, 2019, 11:23 a.m.) |
Indexed | 1 year ago (Aug. 4, 2024, 8:16 p.m.) |
Issued | 21 years, 8 months ago (Dec. 1, 2003) |
Published | 21 years, 8 months ago (Dec. 1, 2003) |
Published Print | 21 years, 8 months ago (Dec. 1, 2003) |
@article{Tang_2003, title={On the Role of Structural Information in Remote Homology Detection and Sequence Alignment: New Methods Using Hybrid Sequence Profiles}, volume={334}, ISSN={0022-2836}, url={http://dx.doi.org/10.1016/j.jmb.2003.10.025}, DOI={10.1016/j.jmb.2003.10.025}, number={5}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Tang, Christopher L. and Xie, Lei and Koh, Ingrid Y.Y. and Posy, Shoshana and Alexov, Emil and Honig, Barry}, year={2003}, month=dec, pages={1043–1062} }